src/jalview/ws/jws1/Annotate3D.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.ws.jws1;
  22
  23 import jalview.datamodel.AlignmentI;
  24 import jalview.io.FileParse;
  25 import jalview.io.FormatAdapter;
  26 import jalview.io.InputStreamParser;
  27 import jalview.util.MessageManager;
  28
  29 import java.io.BufferedReader;
  30 import java.io.FileReader;
  31 import java.io.IOException;
  32 import java.io.InputStreamReader;
  33 import java.io.Reader;
  34 import java.net.MalformedURLException;
  35 import java.net.URL;
  36 import java.net.URLEncoder;
  37 import java.util.Iterator;
  38
  39 public class Annotate3D
  40 {
  41   // protected BufferedReader in;
  42   // protected BufferedWriter out;
  43
  44   public Annotate3D()
  45   {
  46     System.out.println("Annotate3D");
  47     // try {
  48     // Create a URL for the desired page
  49     // String id = "1HR2";
  50     // URL url = new
  51     // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
  52     // in = new BufferedReader(new InputStreamReader(url.openStream()));
  53     // String str;
  54     // OutputStream out1 = null;
  55     // out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
  56     // while ((str = in.readLine()) != null) {
  57     // System.out.println(str);
  58     // out.write(str);
  59     // }
  60     // in.close();
  61     // out.close();
  62     // } catch (MalformedURLException e) {
  63     // } catch (IOException e) {
  64     // }
  65   }
  66
  67   public AlignmentI getRNAMLFor(final FileParse source) throws IOException
  68   {
  69     try
  70     {
  71       StringBuffer sb = new StringBuffer();
  72
  73       Reader fpr = source.getReader();
  74       int p = 0;
  75       char[] cbuff = new char[2048];
  76       while ((p = fpr.read(cbuff)) > 0)
  77       {
  78         for (int i = 0; i < p; i++)
  79         {
  80           sb.append(cbuff[i]);
  81         }
  82       }
  83       Iterator<Reader> r = jalview.ext.paradise.Annotate3D
  84               .getRNAMLForPDBFileAsString(sb.toString());
  85       AlignmentI al = null;
  86       while (r.hasNext())
  87       {
  88         FileParse fp = new InputStreamParser(r.next(), source.getDataName());
  89         AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
  90         if (al == null)
  91         {
  92           al = nal;
  93         }
  94         else
  95         {
  96           al.append(nal);
  97         }
  98       }
  99       return al;
 100     } catch (Throwable x)
 101     {
 102       if (x instanceof IOException)
 103       {
 104         throw ((IOException) x);
 105       }
 106       else
 107       {
 108         throw new IOException(
 109                 MessageManager
 110                         .getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
 111                 x);
 112       }
 113     }
 114   }
 115
 116   public Annotate3D(String path) throws InterruptedException
 117   {
 118     System.out.println("Annotate3D");
 119     try
 120     {
 121       // //URL url = new
 122       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
 123       // System.out.println("Step1");
 124       // FileReader r = new FileReader(inFile);
 125       // BufferedReader in = new BufferedReader(r);
 126       // StringBuffer content = new StringBuffer();
 127       // System.out.println("Step2");
 128       // while(in.readLine()!=null){
 129       // content.append(in.readLine());
 130       // //System.out.println("Step3"+in.readLine());
 131       // }
 132       //
 133       // String data = URLEncoder.encode("data", "UTF-8") + "=" +
 134       // URLEncoder.encode(content.toString(), "UTF-8");
 135       // for (int i=0;i<data.length();i++)
 136       // {
 137       // System.out.print(data.charAt(i));
 138       // }
 139
 140       // String data = "width=50&height=100";
 141
 142       // // Send the request
 143       // FileReader r = new FileReader(path);
 144       // BufferedReader in = new BufferedReader(r);
 145       // StringBuffer content = new StringBuffer();
 146       // System.out.println("Step1");
 147       // while(in.readLine()!=null){
 148       // content.append(in.readLine());
 149       //
 150       // }
 151       // System.out.println("Step2");
 152       // String data = URLEncoder.encode("data", "UTF-8") + "=" +
 153       // URLEncoder.encode(content.toString(), "UTF-8");
 154       // System.out.println("Step2");
 155       // URL url = new
 156       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
 157       // DataInputStream is = new DataInputStream(url.openStream());
 158       // String str;
 159       // while ((str = is.readLine()) != null) {
 160       // System.out.println(str);
 161       // //out.write(str);
 162       // }
 163       FileReader r = new FileReader(path);
 164       BufferedReader in = new BufferedReader(r);
 165       String content = "";
 166       String str;
 167
 168       while ((str = in.readLine()) != null)
 169       {
 170         // System.out.println(str);
 171
 172         content = content + str;
 173       }
 174       System.out.println("pdbfile=" + content.toString());
 175       System.out.println("capacité=" + content.length());
 176       String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
 177       System.out.println("param=" + paramfile);
 178       URL url = new URL(
 179               "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
 180                       + content);
 181       BufferedReader is = new BufferedReader(new InputStreamReader(
 182               url.openStream()));
 183       String str4;
 184       while ((str4 = is.readLine()) != null)
 185       {
 186         System.out.println(str4);
 187         // out.write(str);
 188       }
 189       in.close();
 190       is.close();
 191
 192       // HttpURLConnection connection = (HttpURLConnection)url.openConnection();
 193       // connection.setRequestMethod("POST" );
 194       // connection.setRequestProperty("data", path );
 195       // //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
 196       // BufferedReader input = new BufferedReader(new
 197       // InputStreamReader(connection.getInputStream()));
 198       // //DataInputStream input = new
 199       // DataInputStream(connection.getInputStream());
 200       // String c;
 201       // while((c=input.readLine())!=null){
 202       // System.out.print(c);
 203       // }
 204       // input.close();
 205       // BufferedReader in1 = new BufferedReader(is);
 206
 207       // OutputStream out1 = null;
 208       // System.out.println("Step3");
 209       // BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
 210       // "temp.rnaml"));
 211       //
 212       // in.close();
 213       // out.close();
 214
 215       // return;
 216
 217       // System.out.println(data.length());
 218       // System.out.println("step2");
 219       // URL url = new
 220       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
 221       // System.out.println("step3");
 222       // URLConnection conn = url.openConnection();
 223       // conn.setDoOutput(true);
 224       // OutputStreamWriter writer = new
 225       // OutputStreamWriter(conn.getOutputStream());
 226
 227       // write parameters
 228       // writer.write(data);
 229       // writer.flush();
 230
 231       // Get the response
 232       // StringBuffer answer = new StringBuffer();
 233       // //BufferedReader reader = new BufferedReader(new
 234       // InputStreamReader(conn.getInputStream()));
 235       // //String line;
 236       // while ((line = reader.readLine()) != null) {
 237       // answer.append(line);
 238       // System.out.println(line);
 239       // }
 240       // writer.close();
 241       // reader.close();
 242
 243       // Output the response
 244
 245     } catch (MalformedURLException ex)
 246     {
 247       ex.printStackTrace();
 248     } catch (IOException ex)
 249     {
 250       ex.printStackTrace();
 251     }
 252   }
 253
 254   // in = new BufferedReader(new InputStreamReader(url.openStream()));
 255
 256   // String str;
 257
 258   // out = new FileOutputStream("temp.rnaml");
 259   // out = new BufferedWriter(new FileWriter("temp.rnaml"));
 260
 261   // while ((str = in.readLine()) != null) {
 262   // System.out.println(str);
 263   // out.write(str);
 264   // System.out.println(str);
 265   // in.close();
 266
 267   // out.close();
 268   // } catch (MalformedURLException e) {
 269   // } catch (IOException e) {
 270   // }
 271   //
 272   // }
 273
 274   // public BufferedWriter getReader()
 275   // {
 276   // System.out.println("The buffer");
 277
 278   // return out;
 279
 280   // }
 281
 282 }